I've had a dream for a long time of a base building mechanic revolving around rescuing scientist and engineer NPCs and having them research and develop new tools to help you fight the apocalypse. They would send you out to gather supplies from new labs, which would encourage exploration and reveal a lot more backstory in the process. Some of the things they could develop for you might include things like a small advancement in the efficiency of your power armor, a specialized focusing lens for your laser rifle, or even a new flavor of mutagen.

This would be accompanied by a mechanic that randomly generates obstacles in the world, like unstable portals, roving groups of bandits, opening hellmouths, etc. The scientists would help develop methods to counter these new obstacles, provided you continue to keep them safe and supplied. There could be a balance with this as well, you have the choice of leaving a portal open for an extended time to gather more valuable resources, but you risk having your base sieged by various interdimensional creatures.

Additionally, as part of the end game, there would be more missions involved in establishing contact with other survivors and the remaining military/government structure. Perhaps the government decides they want your group of scientists, and you're forced to give up your researchers, engage in conflict against the government, or use your speech skill to convince them to designate you as a forward operating base.

I would also love to see specialized NPCs as a way to bring back more "pre-cataclysm" style things, like a skilled engineer NPC with a few pieces of equipment can create factory-quality bullets, instead of reloaded ammo.

Just got me a heavy rail rifle and it SUCKS. For some reason I can't hit the broadside of a barn from 15 tiles away even the max range is 60. Was really hoping for something to combat zombie bio weapons and super soldiers.